Beattie is the third agency to lose out after the group's decision to shun agencies for what Bank of Scotland head of media relations Mark Elliott called 'strategic reasons'.
Before the merger of the Bank of Scotland and the Halifax, which took place in 2001, Lansons Communications had handled media relations for BoS's retail banking.
In addition, Brunswick had provided financial PR advice to BoS on a project basis.
Both Lansons and Brunswick have ceased to work for the merged HBOS, with all media relations being handled by group comms general manager Shane O'Riordain's in-house team.
Reporting to O'Riordain are two teams of six, headed by Mark Hemingway in Halifax and Edinburgh-based Elliott.
Beattie Media handled media relations for BoS's corporate and business banking teams, work that is now set to be handled in-house.
'We carried out a strategic review in the run-up to, and shortly after, the merger and we decided we had the skills in-house,' said Elliott.
It was reported last month that Beattie Media was serving out a notice period on its remit for tech giant Hewlett Packard (PRWeek, 31 January).
Beattie founder Gordon Beattie said: 'We have enjoyed working with them and hope to soon announce we have started working with another bank.'
HBOS continues to retain just one agency - Carnegie Worldwide - which handles media relations and event management for BoS's sponsorship deals.
Carnegie, which promotes BoS's link-ups in sport and art - such as sponsorship of the Bank of Scotland Premier League and the Edinburgh International Festival - will continue to be retained, Elliott said.